3 label: RNAseq CWL practice workflow
12 run: bio-cwl-tools/fastqc/fastqc_2.cwl
21 run: bio-cwl-tools/STAR/STAR-Align.cwl
23 RunThreadN: {default: 4}
26 OutSAMtype: {default: BAM}
27 SortedByCoordinate: {default: true}
28 OutSAMunmapped: {default: Within}
32 run: bio-cwl-tools/samtools/samtools_index.cwl
34 bam_sorted: STAR/alignment
35 out: [bam_sorted_indexed]
37 ### 8. Adding it to the workflow
42 run: featureCounts.cwl
44 counts_input_bam: samtools/bam_sorted_indexed
51 outputSource: fastqc/html_file
54 outputSource: samtools/bam_sorted_indexed
56 # Adding it to the workflow
59 outputSource: featureCounts/featurecounts